Berk Hess wrote:
Hi,
That thermostat is really nice and also simple to implement.
It is now in CVS.
If this thermostat has a stochastic term, is the dynamics still
meaningful then?
(I haven't read the paper of course :)).
Thanks for the tip!
Berk.
> Date: Wed, 23 Jul 2008 10:12:36 -0400
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Re: Question about Berendsen thermostat and
Nose-Hoover temp coupling ([EMAIL PROTECTED])
>
> Note that a recently a velocity rescaling algorithm was developed in
> the Parrinello group that does give the correct canonical ensemble.
> See: http://arxiv.org/abs/0803.4060. It might be nice to replace
> Berendsen with this algorithm, which should have the nice properties
> of Berendsen (converges to the constraint temperature quickly) without
> the serious drawbacks.
>
> Cheers,
> Michael
>
> On Wed, Jul 23, 2008 at 10:10 AM, Michael Shirts
> <[EMAIL PROTECTED]> wrote:
> >> Have you seen any information to suggest that this is actually a
> >> non-trivial concern? That is, given static point charges, an empirical
> >> LJ force, short cutoffs, etc., do you believe that the application of
> >> nose-hoover, berendsen, or even the arbitrary velocity rescaling
> >> significantly degrades the quality of the obtained dynamics?
> >
> > 1) I think there's an important distinction to be made here between
> > accuracy and physical validity. If you use a thermostat, then the
> > dynamic properties you obtain for the system will be different than
> > the properties obtained without the thermostat, independent of what
> > model you choose. So, I don't know that it's that useful to ask
> > whether the differences from the true system due to thermostat are
> > large compared to the differences due to the choice of model -- the
> > results are going to be dependent on the thermostat, so the field has
> > chosen a standard definition of the dynamics, one that most resembles
> > the actual physical system (where there isn't temperature rescaling
> > every 2 fs or a piston coupled to a 10 nm cube of water, etc).
> >
> > 2) If one uses the Berendsen thermostat, then statistical mechanics of
> > canonical ensembles will not strictly apply, and one can't use many of
> > the results one would like to (or, are using already incorrectly).
> > One can do physics-based simulation of molecular models, or one can do
> > non-physics-based simulations of molecular models. In many cases, the
> > non-physics-based results will be statistically indistinguishable from
> > the physics based results. But why bother with an uncontrolled
> > approximation when you don't -have- to use one? It just adds another
> > chance that what one simulates is not reproducible or reliable, and
> > heaven knows that simulation currently has enough of those already.
> >
> > It's like building a tower out of blocks, and each uncontrolled
> > approximation, no matter how small, is a bit of unevenness in the
> > block. If you have just one wobbly block, you can stand on it pretty
> > well -- you know the limits of the approximation, you can get a pretty
> > good sense of what's going on with the system. Once there's a large
> > number of wobbly blocks, though -- good luck standing on top of it and
> > trying to build good science. As simulations get larger and more
> > complicated, they are built out of more and more blocks, and we need
> > to make sure we're paying careful attention to how well they all fit
> > together.
> >
> > Best,
> > Michael Shirts
> > Research Fellow
> > Columbia University
> > Department of Chemistry
> >
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